Something Wrong Dear?
by The boy who cried Godzilla
Summary: Well, what do you know, another Doctor's baby fic. Thomas has lived a semi-normal life, but when pepper shaker robots attack him, and a madman in a box shows up to rescue him? things are getting weird. (I suck at summaries don't I?)
1. Chapter 1

**Author's note**- This here, is a mystery, can you figure out which incarnation of the doctor is his father? And which popular companion is his mother? Put your guesses in reviews!

* * *

"Something wrong?" asked the doctor.

She had been in and out of the bathroom all night.

"no." she said.

The next morning She said something rather troubling.

"you want what!?" asked the Doctor.

"I wish to be left on earth for one year."

"but, why!"

"I just need some space doctor."

"If it's something I've done - "

"No, It's not you, It's me, I, I, just have something that needs to be done!"

there were tears in her eyes as she ran from the TARDIS.

The doctor was left dumbfounded. He wondered if it had anything to do with what had occurred between them the night before. He quickly dismissed this notion.

40 weeks later in London...

Kicking. She felt kicking. The pain. The Ambulance came and she was put under. She awoke in he hospital to pain like she had never felt before. And it was ended with the crying of an infant.

For the doctor it was but a second. And when he again opened the TARDIS doors there she was. Like nothing had happened. She ran forward and embraced him, almost knocking him over.

"I missed you!"

"So did I. So did I."

yet half a mile away from that spot, an infant appeared on an orphanage doorstep.

"Thomas Smith?"

13 years later...

"hey Tommy!" a voice cried in the brisk January air.

Thomas sighed and picked up his pace.

"hey facial feature freak! I'm talking to you"

the larger of the two boys grabbed the smaller one's scarf, making him gag.

The larger one grabbed Thomas by his dark, curly hair, and pulled, making him scream the larger then shoved him face down into the snowy asphalt. As Thomas spit the snow from his mouth, the larger boy stomped his head right back in. He then called Thomas some very rude names and fled. Thomas picked himself up, and brushed the snow off of his jacket and retrieved his books from the snow, sighed, and returned to the orphanage, and went to sleep.


	2. Chapter 2

Breakfast the next morning was dreary, but quiet. Thomas valued silence, and it was abundant, now that he was the last boy in the home. All of them were adopted at Christmas. All but Thomas. He did not expect to be adopted, only the babies got adopted. Ages 0-5. Thomas, a boy of 13, was just waiting for his eighteenth birthday, when he could leave, and carve out a life for himself. As the last boy in the home, he was given the privilege to go to a real school. But that one light in his life, was extinguished by the larger boy. Thomas did not even know the boy's name, and he doubted that the boy knew his. Every day, in the alley behind the school, the large boy, would torment Thomas. Thomas placed his bowl into the caretaker's sink (as the last boy, he was allowed to eat in there.) and he gathered his things and left for school, but it was not until he was already there that he remembered that it was Saturday.

"Hey Tommy!"

"Not today. Please." he began to walk back to the orphanage.

"Well then, as' too bad!"

at that moment, Thomas heard a scream.

He looked back and saw that the large boy had fallen to a smoking pile on the ground.

"Collect the Specimen!"

the voice came from a giant space pepper shaker. On this command, two more came and picked up the large boy with a plunger type thing, and they disappeared.

"Earthling Detected! Fire!"

the robot then began to fire at him.

* * *

"Can I see him?" she asked.

"of course you can Mrs. Smith." smiled the nurse.

She held the baby in her hands, looked to see if anyone was watching, and held a strange device up to it. And placed a homing device in his tissue, that would only activate when the baby was in mortal danger, and it also would hide his second heart.

* * *

Inside the TARDIS, the 11th Doctor was locked in a coat closet with a certain Impossible girl.

He was rather enjoying himself until he heard a disturbing sound. The TARDIS was moving. But no one was in the console room. The doctor removed Clara's face from his own, and put a finger on her lips.

"Back in two ticks love."

in the console room, the doctor looked at where that TARDIS was headed.

"1991?"

"what's the deal Doctor?"

"The TARDIS is sending us to 1991."

Clara smiled. "Hotels cheaper then?" she said joking.

"funny." replied the Doctor.

The Doctor Opened the door to the TARDIS, to see a boy running toward him in the snow.

But a look behind him and he saw...

"Daleks?!"

at that moment he was knocked over by a Thirteen-year-old, who was blind with fear.

"S-Sorry s-sir."

The doctor stood up, and put Thomas back on his feet.

"What are those things!"

"Daleks, time traveling cyborgs."

"And why do they want to kill me?"

"not sure."

"are you hurt?"

"umm... no. Why?"

"you have bruises all over your face."

"erm... yes. bruises." said the doctor examining the smudged lipstick on his face in a mirror.

"well, what are we going to do now Doctor?" asked Clara who was perched on the TARDIS console.

"We'll have to fight."


	3. Chapter 3

"something strangely familiar about that kid..." thought the Doctor,

"Okay, here's the plan", said the Doctor, taking some monopoly pieces from his pocket.

"This little top hat, is me, the butter churn is the TARDIS,Clara is the Iron, and you..."

"Thomas."

"Right, so you are this boot."

"so the thimble and everything else is a Dalek."

* * *

later...

"Chaaaaarge!" said the Doctor as himself, Clara, and Thomas ran from the TARDIS.

Thomas ran around the dalek farthest to the left.

"twice around, and dash!" he said to himself, remembering the Doctor's instructions.

Clara and the Doctor were providing a sturdy distraction for the Daleks.

"so this must be the beacon type thing. Could it be anymore obvious?"

Thomas proceeded to turn the beacon off.

"Thanks!" said the doctor.

He proceeded to open the heads of the three daleks, and climbed inside, and instructed the others to do the same.

"what are you doing?" asked the doctor to Thomas as he wrapped his scarf around the Dalek's neck-ish thingy.

"spoils of war. And team identification."

"Why didn't I think of that?" said the Doctor, as he placed his bow-tie on the front of the Dalek.

"not sure what you'll do Clara. Maybe your Jacket or something."

Clara sighed. "fine Doctor."

"Allrighty then, lets move out!"

earlier...

"Okay, so , here's the plan", the Doctor began to move the small pewter monopoly pieces about the floor. "Clara and I will distract them, while you, Thomas, make this Dalek become confused by running around it many times, theese are an older model, so they are going to have a beacon-y thing that will administer electromagnetic pulses through the ground, so that they can move about on non-metal surfaces."

"okay... so what then?" asked Thomas.

"you will turn it off, and we will dispose of the squidy things inside them, and use the shell to return to their ship and find out what's going on here!"

"Ready?"

"ready as I'll ever be." said Clara.

"umm... yes!"

"in that case, CHAAAAAARGE!"


	4. Chapter 4

the three "Daleks" were transported into the Dalek mother ship after their previous escapade was over.

* * *

"Was the mission successful?!"

"Affirmative!"

"I like your Bow-Tie!"

"Thank you!"

"Report to the leader, and report our victory!"

"Can Do!"

"Quite Dalekey doctor." said Clara sarcastically through one of the three way microphones inside the Dalek shells.

"he seemed to buy it."

they then started down the corridor.

"hello there!" said the bow-tied dalek as he stopped and turned into a dark hallway.

"Doctor! What's wrong with you? Dark scary hallways are bad enough without the fact that they are inside a Dalek ship!"

"I agree with Clara."

"did neither of you read the sign?"

"what sign?" asked Clara.

"that big copper sign that said History archives on it!"

"you mean that jibberish above the door?"

"It's not Jibberish, its Kaled!" said the Doctor

"what are we doing in a dalek library?"

"out of date daleks, attacking earth, when they know tthat it's under my protection, this is getting weird."

the Doctor accessed a viewscreen and read a few entries before an alarm sounded.

"RUN!" said the doctor.

But before they got the chance, a small army of Daleks, old and new, encircled them, out of their armor.

"The daleks had the three er- two of us listed as dead, and that they had finally won the time war." the doctor hastily whispered to the two of his companions.

on the way to the Dalek dungeon, Clara had a few questions to ask of the Doctor.

"but why are there a bunch of old daleks here, I thought that they died when new models were made."

"they do, but this is a sort of black ops, an elite squadron, separate from the normal collective."

at that moment, the three were separated, by their Dalek escorts.

"Doctor!" cried Clara.

"I won't let them take you! I'll-I'll come for you!"

"Don't mind me, as I'm taken away to die!" called Thomas as he was carried further down the hallway.

he heard the Doctor yell something in response, but he was too far away to hear.

Later, Thomas found himself bound to a table in a torture chamber.

"tell Us!"

"what?"

"where are the rest of the Time lords!"

"time lords?"

"do not play the alleged ignorance card!"

"what's a time lord!"

"You have tested our patience! Now speak!"

"I have no Idea what you're talking about!"

"and so you have chosen the 'hard way'"!

The Doctor heard the screaming from half way across the ship.

At that moment the doctor felt a burst strength, dormant within him for centuries. He broke out of his shackles, and bashed the torture dalek's dome in, and flew from the chamber.

"EXTERMINATE! EXTERMINATE!EXTERMINATE!"

at that moment, Clara watched as her angel of death's armour began to crack, and green liquid oozed from them. At that moment, the dalek's head fell off to reveal none other than the Doctor.

"Doctor!" said Clara, with tears in her eyes

the doctor used his sonic screwdriver to remove Clara's shackles.

"which way did they take him?"

"Who?"

"Thomas! Was it left?"

"what?"

"did they take him left!"

"I think so!"

the doctor ran from the room.

"How do you know which room he's in?!" said Clara, Holding her Tattered shirt to her body.

"Paternal Instinct!"

"Pat- WHAT!?"

"Hurry Up!"

"Alright, but you've got some _serious_ explaining to do!"

when they reached his hallway, they found it blocked off. The Doctor made quick work of it. Yet his door was open.

The doctor stood poised to destroy another Dalek.

"Gimme that!" said Clara.

The dalek began to rotate, and Clara used her confiscated sonic screwdriver to stop it in it's tracks.

"Hey! Stop!"

"quiet you!" said Clara. And the Dalek stopped talking (she had pressed the sonic button again)

"your awfully quiet." said Clara

the doctor was silent.

"What?"

the doctor mumbled something. At that moment, Clara saw what he saw.

"my god." said Clara. "he was just a kid."

what they saw, in the glass booth before them, was the boy who stumbled into the T ARDIS, at least, what was left of him. His eyes glazed over, and spots of smoldering flesh covering him.

"no."

"what?"

"he's gone."

"what are you crying about?"

the doctor looked at her as if she was completely insane.

"you've said it over and over again. Time."

"we've got a time machine!"

"that's right. We do." a smile spread across the Doctor's face. "we've got a time machine!"

the doctor promptly picked her up, spun her around, and pressed his lips to hers.

"you're _Brilliant_!"

The Doctor took the TARDIS to the small hallway connecting the corridor to the torture chamber. They ran out of the ship.

"lock that door! We don't need the other pair of uses to come in here!"

"okay!"

the doctor had done what he had done to the Dalek before.

"Thomas! Are you all right!"

"yes!"

the doctor quickly removed his shackles.

"say nothing!"

when the TARDIS de-materialized, they found Thomas standing in the console room.


	5. Chapter 5-finale

"I think that it's time to get you home. I'd like to talk to your parents."

"I havent got any. I live at bookworth's home for children"

"really?"

"pitiful, right? Now you want to start treating me like I have some sort of, Incurable disease, correct?"

"you could come with us." suggested the Doctor.

"really?" asked Thomas.

"sure."

"you know you can't just whisk me away right? I'll get on the news, cause mass hysteria, you know."

"I know."

"Okay then. What's the plan."

the doctor took a folded paper from the inner pocket of his jacket unfolded it and pushed it across the console.

"what's this?"asked Thomas. He looked at it closer. "M-my... adoption papers?"

"Yeah. All it needs is your name. Here, here, here, an initial here, and here."

"but , why? You're, living the dream, fighting aliens, traveling through space..."

"and time." added Clara

"why would you want to ruin that, with, the presence of some kid you found in a back-alley?"

"I missed out on your childhood. I want to see you through your teens."

"you have officially stopped making sense."

"the long and short of it is that, you see, well, I'm kind of your-"

(are you ready for the finale? Thomas's mother shall be revealed! This part takes place before the sentence that did not make sense. When the doctor says "He's gone")

"I think It's high time that I got that explanation I asked for."

they walked slowly back to the TARDIS.

"I'll show you"

when they returned to the TADIS the Doctor pressed a small button on the Console and a a hologram emitted from the console.

The pale blue woman who stood before them began to speak, but stopped abruptly to turn off the song which was playing. (Rita Coolidge: All time high)she began to speak again.

"my dearest doctor, If you are seeing this, It can only mean that you have come across a boy with a familiar face. He is our son." tears began to make their way down her cheeks. "I cannot tell you how sorry I am to have to do this. I have left him on earth. In it's year 1978. galactic standard year, 35466. on earth, he will live free of all of the Timelord duties, he will have no machine, by which to travel in time. But, If you are seeing this, that means that all of that has crumbled. When he is born, I will place this homing device in his flesh, it will only activate when his life is truly threatened. As a plus, it shall also hide his left? No, right heart. This pains me. Far more than I suspect that it would ever have hurt you, as I haven't told you. Until now. I love you. I will always love you. Even if I am deceased when you hear this, and I suspect that I am, I will love you. Yet, following gallifrayan marriage law, If we have both regenerated, you shall not have to honor these emotions,." her voice began to choke up. "Goodbye!"

she, then placed one hand on her stomach, and another to her lips, which she then faced palm out.

"Romana." she said, to finish the transmission.

"now do you see?" asked the Doctor. He looked at Clara, who was crying. "I'm going to feel like a jerk for asking this, what's wrong?"

"Like you don't know!" she snapped at him. "but quite frankly, that was like, Hallmark movie beautiful."

"He was the true last of the Timelords."

"*sniff*sniff* How?"

"his mother was a Timelord, mine was not. He had more of a claim to the title of 'the last of the Timelords' than I did."

"wow. I'm sorry." said Clara. She took a strip of cloth from the bottom of her ruined shirt, and dabbed under the Doctor's eyes.

(okay, back to real-time)

"Hello, Madame, I would like to adopt this fine boy!" beamed the Doctor.

"do you have his consent?" said the bored secretary, popping a large gum-bubble.

"Yes, matter-of-fact, I do!"

"okay, take him."

"that's all?" asked the Doctor.

"yep."

"just sign the papers and give them to you?"

"yep. Now get goin' 'fore permanent closing time."

"Okay!"

* * *

Later aboard the TARDIS...

"I like your scarf."

"thanks."

Clara had insisted that they have father-son bonding time.

"mum made it. I think."

"I think she did. Looks just like one of mine."

"one of yours?"

"I used to wear one all the time. I've got an entire room dedicated to scarves."

"where?"

"adjacent to the Bow-tie room. Of course, the ones that I actually wore, are on display in glass cases."

"could we see them?"

"I would, if Clara would let us out of here."

"what were you doing before The whole Dalek thing?"

"we were collecting the jettisoned rooms, because once, I had to eject, many rooms at random, many of which, I needed. a lot."

"Well, what are we waiting for? Let's go find them."

"again, I would, if **CLARA WOULD LET US OUT!**"

the door swung open.

"fine, fine, you can come out." said Clara.

"well, then, lets go."


End file.
